Title

Author

Defense Date

2013

Document Type

Dissertation

Degree Name

Doctor of Philosophy

Department

Human Genetics

First Advisor

Sarah Elsea

Abstract

Neurodevelopmental disorders (NDs) are a growing public health concern. These complex disorders cause failure of normal brain development, which leads to intellectual disability (ID) or autism in 3% of children. Accurate diagnosis of NDs is difficult due to complex overlapping phenotypes. Moreover, associations between phenotypically similar NDs and their overlapping molecular mechanisms remain unidentified. The chromosome 2q23.1 region is a newly discovered disease region. We have recently identified a novel ND, 2q23.1 deletion syndrome. The phenotype includes severe ID, significantly delayed speech, behavioral problems, seizures and short stature. This syndrome shares characteristics in common with other genetic syndromes, including Smith-Magenis (SMS, RAI1), Pitt-Hopkins (PTH, TCF4), Angelman (AS, UBE3A) and Rett (RTT, MECP2) syndromes, including ID, speech impairment, and seizures, in addition to other autism spectrum disorder (ASD)-associated phenotypes (associated with mutation of MBD1). The methyl-CpG binding domain protein 5 (MBD5) is thought to be the causative gene for the core phenotype seen in del2q23. We propose that MBD5 is a dosage dependent gene, wherein deletion or duplication results in two distinct syndromes. We hypothesize that deletions, mutations, and duplications in MBD5 and its associated overlapping gene networks are responsible for causing the phenotype seen in 2q23.1 disorders. Furthermore, we hypothesize that syndromic neurodevelopmental genes are involved in common biological networks that, when dysregulated, result in the overlapping phenotypes present in many of these neurodevelopmental disorders. We first show that the causative gene for 2q23.1 deletion syndrome is MBD5. We established a consortium of clinical diagnostic and research laboratories to accumulate a large cohort with genetic alterations of chromosome 2q23.1, acquiring 65 subjects with microdeletion or translocation. We sequenced translocation breakpoints, aligned microdeletions to determine the critical region, assessed effects on mRNA expression, and examined medical records, photos, and clinical evaluations. We identified MBD5 as the only locus that defined the critical region. Partial or complete deletion of MBD5 was associated with haploinsufficiency, intellectual disability, epilepsy, and autistic features. Sixteen alterations disrupted MBD5 alone, including partial deletions of noncoding regions not typically captured or considered pathogenic by current diagnostic screening. Expression profiles and clinical characteristics were largely indistinguishable between MBD5-specific alteration and deletion of the entire 2q23.1 interval. We surveyed MBD5 coding polymorphisms among 747 ASD subjects compared to 2,043 non-ASD subjects analyzed by whole-exome sequencing and detected an association with a highly conserved methyl-CpG binding domain missense variant, G79E (p=0.012). Thus, we establish that haploinsufficiency of MBD5 is the primary causal factor in 2q23.1 microdeletion syndrome and that mutations in MBD5 are associated with autism. Secondly, we show that MBD5 is a dosage dependent region, wherein deletion or duplication results in altered gene dosage. We previously established the 2q23.1 microdeletion syndrome and report herein 23 individuals with 2q23.1 duplications, thus establishing a complementary duplication syndrome. The observed phenotype includes intellectual disability, motor delay, language impairments, infantile hypotonia and gross motor delay, behavioral problems, autistic features, dysmorphic facial features (pinnae anomalies, arched eyebrows, prominent nose, small chin, thin upper lip), and minor digital anomalies (fifth finger clinodactyly and large broad first toe). The microduplication size varies among all cases and ranges from 680 kb to 53.7 Mb, encompassing a region that includes MBD5. Phenotypic analyses suggest that 2q23.1 duplication results in a slightly less severe phenotype than the reciprocal deletion. The features associated with a deletion, mutation, or duplication of MBD5 and the gene expression changes observed support MBD5 as a dosage sensitive gene critical for normal development. Dup(2)(q23.1) causes a phenotype similar to del(2)(q23.1) and other NDs, like SMS and autism, suggesting shared molecular pathways. Finally, chromatin-modifying genes play an important role in the genetic etiology of many NDs, including intellectual disability, epilepsy, and autism. Many monogenic NDs are caused by chromatin modifying genes, including 2q23.1 deletion and duplication, SMS, RTT, AS, fragile X syndrome (FXS), and PTH. Many of these disorders have overlapping features that include language, sleep, and behavioral anomalies. Investigation of relative gene expression by quantitative PCR and microarray of cell lines from individuals with disorders due to altered expression of MBD5, RAI1, MECP2, UBE3A, TCF4, and MBD1 revealed molecular signatures that allowed for the generation of a novel neurodevelopmental molecular network supporting the overlapping features across these syndromes. Further, knockdown of MBD5 and RAI1 in SH-SY5Y and HEK293T cell lines expanded the repertoire of genes involved in these pathways and showed that other chromatin modifying genes, as well as developmental genes are dysregulated. Pathway analyses showed that MBD5 and RAI1 function in chromatin remodeling, circadian rhythm, neuronal development, and cell growth/survival pathways. From these studies, precise gene dosage of chromatin modifying genes, such as RAI1 and MBD5 are clearly a requirement for normal neurodevelopment and function. Taken together, these studies have given us insight into the role of MBD5 as a dosage sensitive gene in two NDs. Furthermore, we gained insight of how dosage effects of MBD5 and RAI1 affect molecular pathways that are linked to neuronal and behavioral development. We have unveiled pathways and genes, which are important to normal human development, neurodevelopment and behavior. These findings support further investigations into the relationships among causative neurodevelopmental genes, which will lead to common points of regulation that may be targeted toward therapeutic intervention.